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Agneesh Barua
I am a graduate student at the Okinawa Institute of Science and Technology Graduate University (OIST). The main focus of my PhD is evolutionary genetics of complex traits. I use quantitative genetics, phylogenetic comparative methods, genomics, transcriptomics, and network approaches to understand the genetic basis of complex trait evolution.
Education
PhD. Candidate
Okinawa Institute of Science and Technology Graduate University
Okinawa, Japan
current - 2017
- Currently working on the origin of extra-cellular RNA in snake venom.
Msc Genetics
University of Calcutta
Kolkata, India
2015 - 2013
- Thesis: Role of P16/CDKN2A in Glioma: A Molecular Study.
BSc(H) Zoology
University of Delhi
New Delhi, India
2013 - 2010
- Special undergraduate research: Antifungal activity of Phyto-extracts of Piper longum, Aloe vera, and Withania somnifera against human fungal opportunistic pathogen Candida albicans.
Research Experience
Rotation Student
Okinawa Institute of Science and Technology Graduate University
Okinawa, Japan
2017 - 2016
- Bio/Micro/Nano fuidcs Unit, Prof Amy Shen.
- Oncology-Cell signalling Unit, Prof. Tadashi Yamamoto.
- Project- Developing a microfluidic model to study cancer metastasis.
- Role- Involved in identifying a suitable device that could be used to grow various mammalian cells and mimic the tumor-vascular tissue interface, followed by testing the effect of growth factors on the migration of mammalian breast cancer cells.
- Achievements- Successfully developed a model system that could be used to observe changes in migration potential of cells exposed to different growth factors. Received A grade for both rotation projects.
Research Intern
Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University
Okinawa, Japan
2016 - 2016
- Project- Characterising the evolutionary forces behind rapid evolution of snake venom genes.
- Role- Gene annotation of newly sequenced Prothrobothrops mucrosqamatus genome, developing a visualization of transcriptional network using d3, mapping out sequence variants on protein structure using PyMol.
- Achievements- Developed skill sets in evolutionary biology, molecular evolution, bioinformatics, programming. Internship project was published with me as a co-author.
Project Fellow
National Institute of Mental Health and Neuroscience (NIMHANS)
Bangalore, India
2015 - 2015
- Project-Using 2-D-Glucose (2-DG) as an adjuvant to supplement treatment by Temozolomide, in high grade glioma.
- Role- Used various techniques in Cell Culture, cytotoxicology, Immunocytochemistry to study the effects 2-DG had on glioma cells U87.
- Achievement- Developed skill sets in Cell culture, Immunocytochemistry, cytotoxicology. Contributed to the development of a new assay based on Acridine Orange dye treatments to visualize and determine cell damage due to radiation.
Project Assistant
National Institute of Mental Health and Neuroscience (NIMHANS)
Bangalore, India
2015 - 2014
- Project- Molecular genetics of the role of P16/CDKN2A in Glioma
- Role- Collection of blood samples from patient wards, and glioma tissue collection from operating theaters. Carry out DNA extractions, Bisulphide conversion of DNA, MS-PCR, Multiplex PCR.
- Achievements- Gained experience and skills in molecular biology techniques. Both thesis and thesis presentation were awarded an O (Outstanding) grade.
Innovation Project Fellow
Delhi University and Jawarharlal Nehru University
New Delhi, India
2013 - 2012
- Project- Antifungal activity of Phyto-extracts of Piper longum, Aloe vera, and Withania somnifera against human fungal opportunistic pathogen Candida albicans.
- Role- Carried out fungal culture, preparation of plant extracts, and drug assays like MIC, Spot assay, and disc diffusion, also carried out GCMS analysis of plant extracts.
- Achievements- Being selected as an Innovation Project Researcher involved writing a research proposal that was screened by a committee of 5 professors. Over 100 candidates were involved in the process. 10 were selected. Project was published in the Delhi University Journal of Undergraduate Research.
Publications
The parallel origins of vertebrate venom
Agneesh Barua, Ivan Koludarov, Alexander Mikheyev
N/A
2021
- bioRxiv
- https://www.biorxiv.org/content/10.1101/2021.04.26.441528v1
- We show that one the most abundant proteins in saliva and venom are homologous and derived from a single ancestral gene.
An ancient, conserved gene regulatory network led to the rise of oral venom systems
Agneesh Barua & Alexander Mikheyev
N/A
2021
- Proceedings of the National Academy of Sciences
- https://doi.org/10.1073/pnas.2021311118
- The first study of its kind to reveal the conserved genetic framework behind oral venom evolution.
Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates
Agneesh Barua & Alexander Mikheyev
N/A
2020
- Proceedings of the Royal Society B
- https://royalsocietypublishing.org/doi/full/10.1098/rspb.2020.0613
- Tests whether snake venom evolution had a role in species diversification in venomous snakes.
Many options, few solutions: Over 60 my snakes converged on a few optimal venom formulations
Agneesh Barua & Alexander Mikheyev
N/A
2019
- Molecular Biology and Evolution
- https://academic.oup.com/mbe/article/36/9/1964/5492084
- First truly quantitative and comparative approach to understand the evolution of the snake venom phenotype.
Population genomic analysis of a pitviper reveals microevolutionary forces underlying venom chemistry
SD Aird, J Arora, A Barua, L Qiu, K Terada, AS Mikheyev
N/A
2017
- Genome Biology and Evolution
- https://academic.oup.com/gbe/article/9/10/2640/4259791
- This paper shows that both drift and selection contribute to venom evolution in snakes, but their relative magnitudes are different.
Antifungal activity of phyto-extracts of Piper longum, Aloe vera, and Withania somnifera against human fungal opportunistic pathogen Candida albicans
H Kaur, RR Goyal, A Bhattacharya, R Gupta, A Barua, … T Prasad
N/A
2015
- DU Journal of Undergraduate Research and Innovation
- http://journals.du.ac.in/ugresearch/pdf/J9.pdf
- Publication from the Delhi University Innovation Project Scheme
Selected Press
Recommended article
Faculty Opinions
N/A
2021
- PNAS paper recommended in Faculty Opinions
- Experts in evolution and comparative genetics described my idea as a “novel and elegant alternative approach.”
- https://facultyopinions.com/prime/739835180?utm_medium=email&utm_source=prime_follow_faculty#eval793584962
Could humans ever be venomous?
Live Science
N/A
2021
- Coverage of my PNAS paper.
- Experts in the field described my study as- “A real landmark in the field.”
- https://www.livescience.com/could-humans-be-venomous.html
Snake venom evolved in fits and spurts
PNAS Front Matter
N/A
2020
- Coverage of my Proceedings B paper.
- Contains commentry from experts in the field. Paper described as “a rich source of hypotheses for future studies.”
- http://blog.pnas.org/2020/05/snake-venom-evolved-in-fits-and-spurts/
Venom and the mystery of evolution
Asahi Shimbun (Japanese only)
N/A
2020
- Special feature highlighting my journey as a PhD student who uses venom to solve the mysteris of evolution.
- Asahi Shimbun is the second largest circulating newspaper in the world.
- https://globe.asahi.com/article/13581404
Snakes; The best bartenders in the Animal Kingdom?
OIST media release
N/A
2019
- Media release of my first PhD publication.
- https://www.oist.jp/news-center/news/2019/6/14/snakes-best-bartenders-animal-kingdom
Academic Talks
Oxford Venoms and Toxins Conference (Online)
Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates
Oxford, England
2020
European Society for Evolutionary Biolgy
Many options, few solutions: Over 60 my snakes converged on a few optimal venom formulations
Turku, Finalnd
2019
Gordon Conference on Venom Evolution , Function, and Biomedical Applications
Many options, few solutions: Over 60 my snakes converged on a few optimal venom formulations
Vermont, USA
2018
OIST internal seminar series
Many options, few solutions: Over 60 my snakes converged on a few optimal venom formulations
Okinawa, Japan
2018
Awards
Society membership
The American Society of Microbiology
N/A
2014 - 2013
- Won a society membership by placing 1st in an inter-department Power-Point presentation contest.
Best Essay
The Acharya Prafulla Chandra Ray Memorial Science Forum. Calcutta University.
N/A
2013
- Awarded 1st prize for best essay on entitled: Science and Society.
Innovation Project Fellow
Delhi University and Jawarharlal Nehru University
N/A
2012
- Awarded a 12 month fellowship that covered stipend.
Teaching
Mini-course on Phylogentic Comparative Methods
OIST
Okinawa, Japan
2020
- Gave a lecture on the importance and utility of phylogenetic comparative methods.
- Graduate level class.
Ryukyu University Invited Lecture
Ryukyu University
Okinawa, Japan
2020
- Was invited for a special lecture to 1st year undergrad students.
- Lecture was on the origin of life in the ocean.
- Undergraduate level class
Mini-course on quantitative genetics
OIST
Okinawa, Japan
2019 - 2017
- TA and lectured on the Animal Model in quantitative genetics, and mixed models.
- Graduate level class.
OIST Science Challenge
OIST
Okinawa, Japan
2019
- Gave a lecture on Phylogenetics and how gene trees can teach us about about the history of animals.
- Undergraduate level class.
Term course on Introduction to Molecular Biology
OIST
Okinawa, Japan
2018 - 2017
- TA and lectured on a course introducing key concepts in molecular biology meant for non-biologists.
- Undergraduate level class.
Professional Development
Academic Officer
OIST Student Council 2020
N/A
2021 - 2020
- Was elected academic officer of the OIST student assembly.
- Worked closely with different departments within the administration including Graduate School, Presidents Office, and Board of Governors/Councilors.
- Worked with graduate school to formulize Student’s Code of Conduct and Academic Course Streams.
Organizer/Committee member
TEDxOIST
N/A
2018 - 2017
- Organized the first TEDx event at my university in 2017.
- Success of the first event was commemorated by a larger event the following year where I was a part of the advisory committee.
Conservation efforts
Fishing Cat Convervation Alliance
West Bengal, India
2011
- Was involved in conservation of the severly threatened Bengal fishing cat
- Collected field samples, set up camera traps, and produced documentary of fishing can conservation
- http://www.youtube.com/watch?v=Utk9UJYJ3kM
- https://www.youtube.com/watch?v=XGTF-w88BPw